![[Feedback]](/icons/banner/feedbackACT.gif){kind=icon}
![[For Subscribers]](/icons/banner/subscriberACT.gif){kind=icon}
![[Archive]](/icons/banner/archiveACT.gif){kind=icon}
![[Search]](/icons/banner/searchACT.gif){kind=icon}
![[Contents]](/icons/banner/tocACT.gif){kind=icon}
|
|
|
|
|
||
Vol. 12, Issue 2, 323-337, February 2001
and#
*Whitehead Institute for Biomedical Research, Nine Cambridge
Center, Cambridge, Massachusetts 02142; We used genome-wide expression analysis to explore how gene
expression in Saccharomyces cerevisiae is remodeled in
response to various changes in extracellular environment, including
changes in temperature, oxidation, nutrients, pH, and osmolarity. The results demonstrate that more than half of the genome is involved in
various responses to environmental change and identify the global set
of genes induced and repressed by each condition. These data implicate
a substantial number of previously uncharacterized genes in these
responses and reveal a signature common to environmental responses that
involves ~10% of yeast genes. The results of expression analysis
with MSN2/MSN4 mutants support the model
that the Msn2/Msn4 activators induce the common response to
environmental change. These results provide a global description of the
transcriptional response to environmental change and extend our
understanding of the role of activators in effecting this response.
Department of
Biology, Massachusetts Institute of Technology, Cambridge,
Massachusetts 02139; and ¶Howard Hughes Medical Institute,
Department of Molecular Genetics and Cell Biology, University of
Chicago, Chicago, Illinois 60637
These authors made equal contributions.
Present addresses:
MRC Clinical Sciences Centre,
Imperial College School of Medicine, Hammersmith Campus, Du Cane Road,
London W12 ONN, UK;
§LG Chemical Ltd., Research Park,
104-1, Moon Ji-Dong, Song-Gu, Taejon, Korea.
#
Corresponding author. E-mail address:
young{at}WI.MIT.EDU.
This article has been cited by other articles:
|
|
 |
|
  D. Melamed, L. Pnueli, and Y. Arava Yeast translational response to high salinity: Global analysis reveals regulation at multiple levels RNA, July 1, 2008; 14(7): 1337 - 1351. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Mascarenhas, L. C. Edwards-Ingram, L. Zeef, D. Shenton, M. P. Ashe, and C. M. Grant Gcn4 Is Required for the Response to Peroxide Stress in the Yeast Saccharomyces cerevisiae Mol. Biol. Cell, July 1, 2008; 19(7): 2995 - 3007. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. M. Molina-Navarro, L. Castells-Roca, G. Belli, J. Garcia-Martinez, J. Marin-Navarro, J. Moreno, J. E. Perez-Ortin, and E. Herrero Comprehensive Transcriptional Analysis of the Oxidative Response in Yeast J. Biol. Chem., June 27, 2008; 283(26): 17908 - 17918. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. A. Gibney, T. Fries, S. M. Bailer, and K. A. Morano Rtr1 Is the Saccharomyces cerevisiae Homolog of a Novel Family of RNA Polymerase II-Binding Proteins Eukaryot. Cell, June 1, 2008; 7(6): 938 - 948. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. S. Gunasekera, L. N. Csonka, and O. Paliy Genome-Wide Transcriptional Responses of Escherichia coli K-12 to Continuous Osmotic and Heat Stresses J. Bacteriol., May 15, 2008; 190(10): 3712 - 3720. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Yamamoto, Y. Maeda, A. Ikeda, and H. Sakurai Regulation of Thermotolerance by Stress-Induced Transcription Factors in Saccharomyces cerevisiae Eukaryot. Cell, May 1, 2008; 7(5): 783 - 790. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. T. Levine and D. J. Begun Evidence of Spatially Varying Selection Acting on Four Chromatin-Remodeling Loci in Drosophila melanogaster Genetics, May 1, 2008; 179(1): 475 - 485. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Ikeda, A. Kihara, A. Denpoh, and Y. Igarashi The Rim101 Pathway Is Involved in Rsb1 Expression Induced by Altered Lipid Asymmetry Mol. Biol. Cell, May 1, 2008; 19(5): 1922 - 1931. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Luo, A. Gruhler, Y. Liu, O. N. Jensen, and R. C. Dickson The Sphingolipid Long-chain Base-Pkh1/2-Ypk1/2 Signaling Pathway Regulates Eisosome Assembly and Turnover J. Biol. Chem., April 18, 2008; 283(16): 10433 - 10444. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Del Vescovo, V. Casagrande, M. M. Bianchi, E. Piccinni, L. Frontali, C. Militti, V. Fardeau, F. Devaux, C. D. Sanza, C. Presutti, et al. Role of Hog1 and Yaf9 in the transcriptional response of Saccharomyces cerevisiae to cesium chloride Physiol Genomics, March 10, 2008; 33(1): 110 - 120. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Trott, J. D. West, L. Klaic, S. D. Westerheide, R. B. Silverman, R. I. Morimoto, and K. A. Morano Activation of Heat Shock and Antioxidant Responses by the Natural Product Celastrol: Transcriptional Signatures of a Thiol-targeted Molecule Mol. Biol. Cell, March 1, 2008; 19(3): 1104 - 1112. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Haitani and H. Takagi Rsp5 is required for the nuclear export of mRNA of HSF1 and MSN2/4 under stress conditions in Saccharomyces cerevisiae. Genes Cells, February 1, 2008; 13(2): 105 - 116. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-Q. Zhang and R. Rao Global Disruption of Cell Cycle Progression and Nutrient Response by the Antifungal Agent Amiodarone J. Biol. Chem., December 28, 2007; 282(52): 37844 - 37853. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Lenssen, N. Azzouz, A. Michel, E. Landrieux, and M. A. Collart The Ccr4-Not Complex Regulates Skn7 through Srb10 Kinase Eukaryot. Cell, December 1, 2007; 6(12): 2251 - 2259. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. O. Morton, A. Hayes, M. Wilson, B. M. Rash, S. G. Oliver, and P. Coote Global Phenotype Screening and Transcript Analysis Outlines the Inhibitory Mode(s) of Action of Two Amphibian-Derived, {alpha}-Helical, Cationic Peptides on Saccharomyces cerevisiae Antimicrob. Agents Chemother., November 1, 2007; 51(11): 3948 - 3959. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. Valerius, M. Kleinschmidt, N. Rachfall, F. Schulze, S. Lopez Marin, M. Hoppert, K. Streckfuss-Bomeke, C. Fischer, and G. H. Braus The Saccharomyces Homolog of Mammalian RACK1, Cpc2/Asc1p, Is Required for FLO11-dependent Adhesive Growth and Dimorphism Mol. Cell. Proteomics, November 1, 2007; 6(11): 1968 - 1979. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. C. Hurlimann, M. Stadler-Waibel, T. P. Werner, and F. M. Freimoser Pho91 Is a Vacuolar Phosphate Transporter That Regulates Phosphate and Polyphosphate Metabolism in Saccharomyces cerevisiae Mol. Biol. Cell, November 1, 2007; 18(11): 4438 - 4445. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Cheetham, D. A. Smith, A. da Silva Dantas, K. S. Doris, M. J. Patterson, C. R. Bruce, and J. Quinn A Single MAPKKK Regulates the Hog1 MAPK Pathway in the Pathogenic Fungus Candida albicans Mol. Biol. Cell, November 1, 2007; 18(11): 4603 - 4614. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. de la Vega, M. R. Hall, K. J. Wilson, A. Reverter, R. G. Woods, and B. M. Degnan Stress-induced gene expression profiling in the black tiger shrimp Penaeus monodon Physiol Genomics, September 11, 2007; 31(1): 126 - 138. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Ren, A. Santhanam, P. Lee, A. Caplan, and S. Garrett Alteration of the Protein Kinase Binding Domain Enhances Function of the Saccharomyces cerevisiae Molecular Chaperone Cdc37 Eukaryot. Cell, August 1, 2007; 6(8): 1363 - 1372. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Yamamoto, J. Ueda, N. Yamamoto, N. Hashikawa, and H. Sakurai Role of Heat Shock Transcription Factor in Saccharomyces cerevisiae Oxidative Stress Response Eukaryot. Cell, August 1, 2007; 6(8): 1373 - 1379. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Sekine, A. Kawaguchi, Y. Hamano, and H. Takagi Desensitization of Feedback Inhibition of the Saccharomyces cerevisiae {gamma}-Glutamyl Kinase Enhances Proline Accumulation and Freezing Tolerance Appl. Envir. Microbiol., June 15, 2007; 73(12): 4011 - 4019. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-P. Hong and M. Carlson Regulation of Snf1 Protein Kinase in Response to Environmental Stress J. Biol. Chem., June 8, 2007; 282(23): 16838 - 16845. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. C. Georg and S. L. Gomes Transcriptome Analysis in Response to Heat Shock and Cadmium in the Aquatic Fungus Blastocladiella emersonii Eukaryot. Cell, June 1, 2007; 6(6): 1053 - 1062. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Mendes-Ferreira, M. del Olmo, J. Garcia-Martinez, E. Jimenez-Marti, A. Mendes-Faia, J. E. Perez-Ortin, and C. Leao Transcriptional Response of Saccharomyces cerevisiae to Different Nitrogen Concentrations during Alcoholic Fermentation Appl. Envir. Microbiol., May 1, 2007; 73(9): 3049 - 3060. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. B. Plotkin and H. B. Fraser Assessing the Determinants of Evolutionary Rates in the Presence of Noise Mol. Biol. Evol., May 1, 2007; 24(5): 1113 - 1121. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Godard, A. Urrestarazu, S. Vissers, K. Kontos, G. Bontempi, J. van Helden, and B. Andre Effect of 21 Different Nitrogen Sources on Global Gene Expression in the Yeast Saccharomyces cerevisiae Mol. Cell. Biol., April 15, 2007; 27(8): 3065 - 3086. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. I. Kanin, R. T. Kipp, C. Kung, M. Slattery, A. Viale, S. Hahn, K. M. Shokat, and A. Z. Ansari Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis PNAS, April 3, 2007; 104(14): 5812 - 5817. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. Hackney, G. M. Ehrenkaufer, and U. Singh Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference Nucleic Acids Res., April 1, 2007; 35(7): 2141 - 2152. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. L. Tai, I. Snoek, M. A. H. Luttik, M. J. H. Almering, M. C. Walsh, J. T. Pronk, and J.-M. Daran Correlation between transcript profiles and fitness of deletion mutants in anaerobic chemostat cultures of Saccharomyces cerevisiae Microbiology, March 1, 2007; 153(3): 877 - 886. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Guo, R. E. Weiss, X. Gu, and M. A. Suchard Time Squared: Repeated Measures on Phylogenies Mol. Biol. Evol., February 1, 2007; 24(2): 352 - 362. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Serrano, H. Martin, A. Casamayor, and J. Arino Signaling Alkaline pH Stress in the Yeast Saccharomyces cerevisiae through the Wsc1 Cell Surface Sensor and the Slt2 MAPK Pathway J. Biol. Chem., December 29, 2006; 281(52): 39785 - 39795. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Fontanesi, I. C. Soto, D. Horn, and A. Barrientos Assembly of mitochondrial cytochrome c-oxidase, a complicated and highly regulated cellular process Am J Physiol Cell Physiol, December 1, 2006; 291(6): C1129 - C1147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Simoes, N. P. Mira, A. R. Fernandes, and I. Sa-Correia The SPI1 Gene, Encoding a Glycosylphosphatidylinositol-Anchored Cell Wall Protein, Plays a Prominent Role in the Development of Yeast Resistance to Lipophilic Weak-Acid Food Preservatives Appl. Envir. Microbiol., November 1, 2006; 72(11): 7168 - 7175. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. L. Eastmond and H. C. M. Nelson Genome-wide Analysis Reveals New Roles for the Activation Domains of the Saccharomyces cerevisiae Heat Shock Transcription Factor (Hsf1) during the Transient Heat Shock Response J. Biol. Chem., October 27, 2006; 281(43): 32909 - 32921. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Thalamuthu, I. Mukhopadhyay, X. Zheng, and G. C. Tseng Evaluation and comparison of gene clustering methods in microarray analysis Bioinformatics, October 1, 2006; 22(19): 2405 - 2412. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Shenton, J. B. Smirnova, J. N. Selley, K. Carroll, S. J. Hubbard, G. D. Pavitt, M. P. Ashe, and C. M. Grant Global Translational Responses to Oxidative Stress Impact upon Multiple Levels of Protein Synthesis J. Biol. Chem., September 29, 2006; 281(39): 29011 - 29021. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L.-C. Lai, A. L. Kosorukoff, P. V. Burke, and K. E. Kwast Metabolic-State-Dependent Remodeling of the Transcriptome in Response to Anoxia and Subsequent Reoxygenation in Saccharomyces cerevisiae. Eukaryot. Cell, September 1, 2006; 5(9): 1468 - 1489. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Belle, A. Tanay, L. Bitincka, R. Shamir, and E. K. O'Shea Quantification of protein half-lives in the budding yeast proteome PNAS, August 29, 2006; 103(35): 13004 - 13009. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. J. Zanton and B. F. Pugh Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock. Genes & Dev., August 15, 2006; 20(16): 2250 - 2265. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Hernandez-Lopez, F. Randez-Gil, and J. A. Prieto Hog1 Mitogen-Activated Protein Kinase Plays Conserved and Distinct Roles in the Osmotolerant Yeast Torulaspora delbrueckii. Eukaryot. Cell, August 1, 2006; 5(8): 1410 - 1419. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. W. Trotter, E. J. Collinson, I. W. Dawes, and C. M. Grant Old Yellow Enzymes Protect against Acrolein Toxicity in the Yeast Saccharomyces cerevisiae. Appl. Envir. Microbiol., July 1, 2006; 72(7): 4885 - 4892. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-O. De Craene, J. Coleman, P. Estrada de Martin, M. Pypaert, S. Anderson, J. R. Yates III, S. Ferro-Novick, and P. Novick Rtn1p Is Involved in Structuring the Cortical Endoplasmic Reticulum Mol. Biol. Cell, July 1, 2006; 17(7): 3009 - 3020. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Swynghedauw Phenotypic plasticity of adult myocardium: molecular mechanisms J. Exp. Biol., June 15, 2006; 209(12): 2320 - 2327. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Delgado-Jarana, S. Sousa, F. Gonzalez, M. Rey, and A. Llobell ThHog1 controls the hyperosmotic stress response in Trichoderma harzianum Microbiology, June 1, 2006; 152(6): 1687 - 1700. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Stolovicki, T. Dror, N. Brenner, and E. Braun Synthetic Gene Recruitment Reveals Adaptive Reprogramming of Gene Regulation in Yeast Genetics, May 1, 2006; 173(1): 75 - 85. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Bachand, D. H. Lackner, J. Bahler, and P. A. Silver Autoregulation of ribosome biosynthesis by a translational response in fission yeast. Mol. Cell. Biol., March 1, 2006; 26(5): 1731 - 1742. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Swaminathan, T. Masek, C. Molin, M. Pospisek, and P. Sunnerhagen Rck2 Is Required for Reprogramming of Ribosomes during Oxidative Stress Mol. Biol. Cell, March 1, 2006; 17(3): 1472 - 1482. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Enjalbert, D. A. Smith, M. J. Cornell, I. Alam, S. Nicholls, A. J.P. Brown, and J. Quinn Role of the Hog1 Stress-activated Protein Kinase in the Global Transcriptional Response to Stress in the Fungal Pathogen Candida albicans Mol. Biol. Cell, February 1, 2006; 17(2): 1018 - 1032. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. V. Antonov, I. V. Tetko, and H. W. Mewes A systematic approach to infer biological relevance and biases of gene network structures Nucleic Acids Res., January 10, 2006; 34(1): e6 - e6. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. D. Rand and C. M. Grant The Thioredoxin System Protects Ribosomes against Stress-induced Aggregation Mol. Biol. Cell, January 1, 2006; 17(1): 387 - 401. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Santos, M. del Mar Alvarez, M. S. Mauro, C. Abrusci, and D. Marquina The Transcriptional Response of Saccharomyces cerevisiae to Pichia membranifaciens Killer Toxin J. Biol. Chem., December 23, 2005; 280(51): 41881 - 41892. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. C. Foat, S. S. Houshmandi, W. M. Olivas, and H. J. Bussemaker Profiling condition-specific, genome-wide regulation of mRNA stability in yeast PNAS, December 6, 2005; 102(49): 17675 - 17680. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Rao, Y. Shibata, B. D. Strahl, and J. D. Lieb Dimethylation of Histone H3 at Lysine 36 Demarcates Regulatory and Nonregulatory Chromatin Genome-Wide Mol. Cell. Biol., November 1, 2005; 25(21): 9447 - 9459. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. K. Vyas, C. D. Berkey, T. Miyao, and M. Carlson Repressors Nrg1 and Nrg2 Regulate a Set of Stress-Responsive Genes in Saccharomyces cerevisiae Eukaryot. Cell, November 1, 2005; 4(11): 1882 - 1891. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Conesa, R. Ruotolo, P. Soularue, T. A. Simms, D. Donze, A. Sentenac, and G. Dieci Modulation of Yeast Genome Expression in Response to Defective RNA Polymerase III-Dependent Transcription Mol. Cell. Biol., October 1, 2005; 25(19): 8631 - 8642. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. P. Nittler, D. Hocking-Murray, C. K. Foo, and A. Sil Identification of Histoplasma capsulatum Transcripts Induced in Response to Reactive Nitrogen Species Mol. Biol. Cell, October 1, 2005; 16(10): 4792 - 4813. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Vanderauwera, P. Zimmermann, S. Rombauts, S. Vandenabeele, C. Langebartels, W. Gruissem, D. Inze, and F. Van Breusegem Genome-Wide Analysis of Hydrogen Peroxide-Regulated Gene Expression in Arabidopsis Reveals a High Light-Induced Transcriptional Cluster Involved in Anthocyanin Biosynthesis Plant Physiology, October 1, 2005; 139(2): 806 - 821. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. A. Petti and G. M. Church A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae Genome Res., September 1, 2005; 15(9): 1298 - 1306. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Bourges, S. Horan, and B. Meunier Effect of Inhibition of the bc1 Complex on Gene Expression Profile in Yeast J. Biol. Chem., August 19, 2005; 280(33): 29743 - 29749. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
|
